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nf-core_modules/tests/modules/gatk4
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Adam Talbot 009f7c691c
Add module: gatk4/leftalignandtrimvariants (#1808) 
* Added: gatk4/leftalignandtrimvariants

Additions:
 - GATK4/LeftAlignAndTrimVariants module
 - Use sars-ncov2 test data as this normalises a larger INDEL correctly.

Fixes #1801

* fixup: Added index to output spec

* fixup: Pattern of tbi output corrected to 'tbi'

* gatk4/leftalignandtrimvariants: Added intervals

Changes:
 - gatk4/leftalignandtrimvariants now supports optional interval as BED
 file
 - Tests added with and without interval. Not test BED file excludes all
 variants so no variants are actually normalised.

Fixes #1801

* fixup: leftalignandtrimvariants vcf->tbi fix

* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
2022-06-28 10:44:08 +02:00
..
applybqsr Update md5sums 2022-05-12 16:07:12 +02:00
applybqsrspark remove variable checksum 2022-06-09 15:44:12 +02:00
applyvqsr Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
baserecalibrator Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
baserecalibratorspark Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
bedtointervallist Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
calculatecontamination Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
calibratedragstrmodel add threads to calibratedragstrmodel 2022-06-07 12:11:18 +02:00
cnnscorevariants add brackets to contains 2022-05-23 13:19:42 +02:00
combinegvcfs double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
composestrtablefile linting 2022-06-01 09:20:20 +02:00
createsequencedictionary Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
createsomaticpanelofnormals Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
estimatelibrarycomplexity Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
fastqtosam Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
filtermutectcalls Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
filtervarianttranches test path update 2022-05-23 12:53:36 +02:00
gatherbqsrreports Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
gatherpileupsummaries Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
genomicsdbimport Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
genotypegvcfs fix test input 2022-05-12 17:37:06 +02:00
getpileupsummaries getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
haplotypecaller Update tests/modules/gatk4/haplotypecaller/test.yml 2022-06-02 14:20:15 +02:00
indexfeaturefile Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
intervallisttobed Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
intervallisttools Update md5sums 2022-05-12 16:07:12 +02:00
learnreadorientationmodel Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
leftalignandtrimvariants Add module: gatk4/leftalignandtrimvariants (#1808) 2022-06-28 10:44:08 +02:00
markduplicates Update md5sums 2022-05-12 16:07:12 +02:00
markduplicatesspark add versions.yml 2022-06-07 14:38:43 +02:00
mergebamalignment fix datatest for stubs 2022-05-06 15:34:18 +02:00
mergemutectstats Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
mergevcfs Updating test for gatk4/mergevcfs 2022-05-31 13:59:56 +00:00
mutect2 fix datatest for stubs 2022-05-06 15:34:18 +02:00
reblockgvcf fix test.yml 2022-06-09 15:14:37 +02:00
revertsam fix datatest for stubs 2022-05-06 15:34:18 +02:00
samtofastq fix datatest for stubs 2022-05-06 15:34:18 +02:00
selectvariants Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
splitintervals removed versions checksum 2022-05-13 14:27:59 +02:00
splitncigarreads Update md5sums 2022-05-12 16:07:12 +02:00
variantfiltration Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
variantrecalibrator Update md5sums 2022-05-12 16:07:12 +02:00